During the debate in the House of Commons over the decision whether to have a referendum over the EUTreaty of Lisbon (5 March 2008), Davidson drew jeers from his Labour colleagues for branding New Labour supporters "Maoists and Trotskyists". Davidson was putting forward the case for disobeying the party line and voting for a referendum.

In June 2011, Davidson accused the Scottish National Party of "narrow neo-fascism". The choice of language resulted in the Labour Party distancing itself from Davidson's comments, saying the use of the word "neo-fascist" was unacceptable, even in the heat of debate,[6] and Angus Robertson to call on him to resign as chair of the Scottish Affairs Select Committee.[7]

On 25 October 2011 it was alleged that Ian Davidson had threatened to inflict "a doing" upon fellow committee member Eilidh Whiteford if details of the committee's discussions during a private session were leaked to the media. Following the allegations Dr Whiteford withdrew from the committee and a formal complaint was made by the SNP Parliamentary Leader, Angus Robertson, to the Speaker of the House.[8] Davidson made a public apology to the committee "for any offence that might have been caused" by his remarks but continued to deny that the remarks had been in any way threatening.[9] Liberal Democrat, Labour and Conservative committee members all stated that no threats were made.[10][11][12] After an investigation the Labour Party stated that it amounted to a "smear campaign" against Davidson due to the forthcoming investigations chaired by Davidson into the SNP's referendum proposal.[13]

A member of the SNP politician Joan McAlpine's staff, Gail Lythgoe, was found to have emailed a women's equality group, supporting Whiteford and alleging that Davidson has a history of bullying women and called on them to demonstrate against him whilst asking them not to reveal SNP involvement in its instigation.[14][15] The email was later leaked and Lythgoe publicly apologised for making unsubstantiated allegations, with the Labour Party alleging that this was a result of an SNP "dirty tricks campaign" against Davidson and calling for an investigation.[14]

In September 2013, Davidson caused anger after he suggested the debate on Scottish independence was continuing only "in the sense there is a large number of wounded still to be bayoneted"[16]

During the 2009-10 Expenses Scandal, it emerged that Davidson claimed £87,699 in the four years to 2007; only £30 below the maximum permitted. He has since admitted that he wished he had a larger mortgage on his London flat to allow him to claim more in allowances and that new expenses rules, brought in after the expenses scandal, would leave him out of pocket. He also used £5,500 of public cash to pay a friend to carry out some renovating work at his flat – he later took the same friend shooting at an annual Commons v Lords competition.[17]